Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)

Wheat breeders and academics alike use single nucleotide polymorphisms (SNP s) as molecular markers to characterize regions of interest within the hexaploid wheat genome. A number of SNP ‐based genotyping platforms are available, and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated data sets. We predict that genotyping by sequencing will become the predominant genotyping technology within the next 5–10 years. With this in mind, to ensure that data generated from current genotyping platforms continues to be of use, we have designed and utilized SNP ‐based capture probes from several thousand existing and publicly available probes from Axiom® and KASP ? genotyping platforms. We have validated our capture probes in a targeted genotyping by sequencing protocol using 31 previously genotyped UK elite hexaploid wheat accessions. Data comparisons between targeted genotyping by sequencing, Axiom® array genotyping and KASP ? genotyping assays, identified a set of 3256 probes which reliably bring together targeted genotyping by sequencing data with the previously available marker data set. As such, these probes are likely to be of considerable value to the wheat community. The probe details, full probe sequences and a custom built analysis pipeline may be freely downloaded from the CerealsDB website (http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB /sequence_capture.php).     

The β3‐integrin endothelial adhesome regulates microtubule‐dependent cell migration

Integrin β3 is seen as a key anti‐angiogenic target for cancer treatment due to its expression on neovasculature, but the role it plays in the process is complex; whether it is pro‐ or anti‐angiogenic depends on the context in which it is expressed. To understand precisely β3's role in regulating integrin adhesion complexes in endothelial cells, we characterised, by mass spectrometry, the β3‐dependent adhesome. We show that depletion of β3‐integrin in this cell type leads to changes in microtubule behaviour that control cell migration. β3‐integrin regulates microtubule stability in endothelial cells through Rcc2/Anxa2‐driven control of active Rac1 localisation. Our findings reveal that angiogenic processes, both in vitro and in vivo, are more sensitive to microtubule targeting agents when β3‐integrin levels are reduced.     

Tropical forests are thermally buffered despite intensive selective logging

Tropical rainforests are subject to extensive degradation by commercial selective logging. Despite pervasive changes to forest structure, selectively logged forests represent vital refugia for global biodiversity. The ability of these forests to buffer temperature‐sensitive species from climate warming will be an important determinant of their future conservation value, although this topic remains largely unexplored. Thermal buffering potential is broadly determined by: (i) the difference between the “macroclimate” (climate at a local scale, m to ha) and the “microclimate” (climate at a fine‐scale, mm to m, that is distinct from the macroclimate); (ii) thermal stability of microclimates (e.g. variation in daily temperatures); and (iii) the availability of microclimates to organisms. We compared these metrics in undisturbed primary forest and intensively logged forest on Borneo, using thermal images to capture cool microclimates on the surface of the forest floor, and information from dataloggers placed inside deadwood, tree holes and leaf litter. Although major differences in forest structure remained 9–12 years after repeated selective logging, we found that logging activity had very little effect on thermal buffering, in terms of macroclimate and microclimate temperatures, and the overall availability of microclimates. For 1°C warming in the macroclimate, temperature inside deadwood, tree holes and leaf litter warmed slightly more in primary forest than in logged forest, but the effect amounted to <0.1°C difference between forest types. We therefore conclude that selectively logged forests are similar to primary forests in their potential for thermal buffering, and subsequent ability to retain temperature‐sensitive species under climate change. Selectively logged forests can play a crucial role in the long‐term maintenance of global biodiversity.     

Oral Glucose Tolerance is Associated with Neuroelectric Indices of Attention Among Adults with Overweight and Obesity

Objective

This study aimed to elucidate the relationship between glucose levels and insulin resistance and sensitivity obtained from oral glucose tolerance tests and neurophysiological indices of attention among adults with overweight and obesity.

Methods

Forty adults with overweight or obesity (BMI ≥ 25 kg/m²) underwent dual‐energy x‐ray absorptiometry to assess visceral adipose tissue. Repeated venous blood samples were collected during an oral glucose tolerance test to measure insulin resistance (homeostatic model assessment of insulin resistance) and indices of insulin sensitivity (Matsuda index and Stumvoll metabolic clearance rate). Attention was assessed using event‐related brain potentials recorded during a visual oddball task. Amplitude and latency of the P3 wave form in a central‐parietal region of interest were used to index attentional resource allocation and information processing speed.

Results

Following adjustment for visceral adipose tissue, reduced values of Matsuda index and Stumvoll metabolic clearance rate (indicating poor insulin sensitivity) were correlated with longer peak latency, whereas insulin area under the curve was positively related to peak latency, indicating slower information processing. Individuals with decreased insulin sensitivity (Matsuda index < 4.3) had significantly longer P3 latencies compared with individuals with normal insulin sensitivity.

Conclusions

Higher fasting glucose, but not homeostatic model assessment of insulin resistance, and reduced indices of glucose sensivity are associated with decrements in attention characterized by slower reaction time and slower information processing speed among adults with overweight and obesity.

     

Variation in coral-associated cryptofaunal communities across spatial scales and environmental gradients

Coral Reefs - Most of the diversity on coral reefs is in the cryptofauna, the hidden organisms that inhabit the interstitial spaces of corals and other habitat-forming benthos. However, little is...     

Hindered transport of macromolecules in isolated glomeruli. II. Convection and pressure effects in basement membrane.

The filtration rates for water and a polydisperse mixture of Ficoll across films of isolated glomerular basement membrane (GBM) were measured to characterize convective transport across this part of the glomerular capillary wall. Glomeruli were isolated from rat kidneys and the cells were removed by detergent lysis, leaving a preparation containing almost pure GBM that could be consolidated into a layer at the base of a small ultrafiltration cell. A Ficoll mixture with Stokes-Einstein radii ranging from about 2.0 to 7.0 nm was labeled with fluorescein, providing a set of rigid, spherical test macromolecules with little molecular charge. Filtration experiments were performed at two physiologically relevant hydraulic pressure differences (delta P), 35 and 60 mmHg. The sieving coefficient (filtrate-to-retentate concentration ratio) for a given size of Ficoll tended to be larger at 35 than at 60 mmHg, the changes being greater for the smaller molecules. The Darcy permeability also varied inversely with pressure, averaging 1.48 +/- 0.10 nm2 at 35 mmHg and 0.82 +/- 0.07 nm2 at 60 mmHg. Both effects could be explained most simply by postulating that the intrinsic permeability properties of the GBM change in response to compression. The sieving data were consistent with linear declines in the hindrance factors for convection and diffusion with increasing pressure, and correlations were derived to relate those hindrance factors to molecular size and delta P. Comparisons with previous Ficoll sieving data for rats in vivo suggest that the GBM is less size-restrictive than the cell layers, but that its contribution to the overall size selectivity of the barrier is not negligible. Theoretical predictions of the Darcy permeability based on a model in which the GBM is a random fibrous network consisting of two populations of fibers were in excellent agreement with the present data and with ultrastructural observations in the literature.     

Salt-induced changes in protein composition in light-grown callus of Mesembryanthemum crystallinum

The halophyte Mesembryanthemum crystallinum (ice plant) has been suggested as a model for salt-tolerance in higher plants. To investigate salt-induced changes in polypeptide patterns at the cellular level, a light-grown callus of M. crystallinum with substantial chlorophyll content, was established and the effect of NaCl on the composition of phenol-extracted protein was examined by SDS- and 2D-polyacrylamide gel electrophoresis (PAGE). SDS-PAGE showed the accumulation of five polypeptides with estimated molecular masses of 40, 34, 32, 29 and 14 kDa was enhanced by the addition of 200 m M NaCl to the culture media. The addition of ABA (10 μ M ) or mannitol (400 m M ) did not elicit the same degree of accumulation of these salt-specific proteins. These polypeptides were classified into two groups according to their course of induction: early responsive (40, 34, 29 kDa) and late-responsive (32, 14 kDa) proteins. In addition, two polypeptides (20, 18 kDa) were transiently accumulated during salt treatment. Further separation of soluble proteins by 2-D gel electrophoresis, either isoelectric focusing (IEF) or non-equilibrium pH-gradient electrophoresis (NEPHGE) followed by SDS-PAGE, showed more alterations in accumulation of polypeptides by NaCl than 1-D gel electrophoresis. Overall, levels of more than 30% of basic polypeptides, detected by NEPHGE/SDS-PAGE, were altered by 200 m M NaCl treatment, while only 10% of neutral and acidic polypeptides, detected by IEF/SDS-PAGE, were changed. The enhanced expression of these proteins by salt in cultured cells is most likely related to the cellular responses to salinity, and not to the mechanism of CAM induction in this facultative halophyte.     

Reproducibility testing of RAPD,AFLP and SSR markers in plants by a network of European laboratories

A number of PCR-based techniques can be used to detect polymorphisms in plants. For their wide-scale usage in germplasm characterisation and breeding it is important that these marker technologies can be exchanged between laboratories, which in turn requires that they can be standardised to yield reproducible results, so that direct collation and comparison of the data are possible. This article describes a network experiment involving several European laboratories, in which the reproducibility of three popular molecular marker techniques was examined: random-amplified fragment length polymorphism (RAPD), amplified fragment length polymorphism (AFLP) and sequence-tagged microsatellites (SSR). For each technique, an optimal system was chosen, which had been standardised and routinely used by one laboratory. This system (genetic screening package) was distributed to different participating laboratories in the network and the results obtained compared with those of the original sender. Different experiences were gained in this exchange experiment with the different techniques. RAPDs proved difficult to reproduce. For AFLPs, a single-band difference was observed in one track, whilst SSR alleles were amplified by all laboratories, but small differences in their sizing were obtained.     

Detection, distribution and probable fate of Escherichia coli O157 from asymptomatic cattle on a dairy farm

The use of commercial anti- Escherichia coli O157-labelled magnetic beads was investigated to improve detection of E. coli O157 by immunomagnetic separation (IMS) from a range of environments on a dairy farm. Immunomagnetic separation proved effective for separation of target cells from laboratory mixtures and during stress in sterile and non-sterile pond water. The IMS procedure was possible with a range of samples (water, faeces, slurry, grass and soil). Non-specific binding of non-target bacterial cells proved problematic in a number of sample types. However, indigenous E. coli O157 cells were detected from samples with a high faecal load, and only with use of IMS. Data on the probable survival and spread of the organism around the farm environment are also discussed.     

Synthesis and biological studies of 5-aminolevulinic acid-containing dendrimers for photodynamic therapy.

Using a convergent growth approach, a series of novel 5-aminolevulinic acid (ALA)-containing dendrimers have been synthesized. In these molecules, ALA residues are attached to the periphery by ester linkages, with amide bonds connecting the dendrons. Three first-generation dendrimers, bearing either 6 or 9 ALA residues, were synthesized by attachment of a tris(Boc-protected ALA)-containing wedge (1) to a di- or tripodent aromatic, or tripodent aliphatic core. Two second generation 18-ALA-containing dendrimers were also synthesized using a 3,3'-iminodipropionic acid spacer unit between wedge 1 and the aromatic core. These compounds differed only in the distance between the core and the linker unit. The Boc-protected dendrimers were deprotected using trifluoroacetic acid and isolated as their TFA salts. The potential of these ALA ester dendrimers as macromolecular prodrugs for photodynamic therapy has been demonstrated in the tumorigenic keratinocyte PAM 212 cell line.